Processing Server External Packages Installation »
Typical Appion workflow package requirement of Appion scripts¶
Appion python scripts are often wrappers that calls scripts or command from other packages. List here are what is needed by each typically used options. Note that users may not want to use all functions as programs go out of fashion.
Direct Detector Frame Alignment¶
appion script name
external package
script/command within the package
makeDDAlignMotionCor2_UCSF.py
MotionCor2
makeDDAlignMotionCorr_Purdue.py
motioncorr v2.0 from Purdue
makeDEAlignedSum.py
deProcessFrames.py
makeDEAlignedSum.py
EMAN2
Automated CTF Estimation¶
appion script name
external package
ctffind4.py
CTFFIND4
gctf.py
Gctf
Particle Selection¶
templateCorrelator.py
template-based particle selection
FindEM
gAutomatchFast.py
template-based particle selection
Gautomatch
Particle Stack Making and manipulation¶
appion script name
subfunction
package
script/command within the package
general image manipulation
EMAN1
proc2d
makestack2.py
making Imagic stack
appionlib
makestack2.py
making Relion stack
Relion
relion_preprocess or relion_preprocess_mpi
makestack2.py
CTF correction by Wiener filtering of the full image (Imagic stack only)
ace2
ace2correct.exe
makestack2.py
normalization by edge
appionlib
makestack2.py/quickstack.py
making montage of stack mean/standard deviation map
ImageMagick
montage
centerParticleStack.py
particle centering in a stack
EMAN1
centeralignint
boxMaskStack.py
soft masking of helical boxed particles in the stack
Spider
sortJunkStack.py
sort particle by similarity to average
Xmipp2
xmipp_sort_by_statistics
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Updated by Anchi Cheng over 6 years ago
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